TBH, I like the idea of the umbilical on the bottom better then it obstructing the ladder or the RCS, but maybe you could try rotating it a little bit further then on Orion, into that empty space below the window.

If it's the SDHI SMS, you'll be happy to know that @sumghai is working on a new version that is designed to mate with the 1-3, but you can still use the 1-3 with the current version, if you don't mind the BPC hatch and umbilical not lining up.

my mom still thinks that CDs can pass viruses between computers, or that barring that, malicious parties could put viruses on CDs at the factory, she also refuses to allow any of her software to update because she's afraid it will stop working on her computer and "it works fine as it is." Yes, using software that isn't trusted can be harmful to your computer, but so could normal use. It's smart to be careful what and where you download, but fearing the risks can be just as harmful.
In general, any mod you download from a community like this is probably safe, just avoid the more sketchy sites.

procedural fairings has a script that automatically removes the 2.5 and 3.75 meter fairings and changes the 1.25 meter one to work like their fairings (does not seem to effect the 5 meter MH fairing base). I know it's rather annoying, since there's some times where the stock fairings are still useful, and it breaks any rocket that uses stock fairings. To get the stock fairings back, delete PF_Squad_Config.cfg.

I'm not worried about what the spent stage actually does while it's still in physics range (as long as it doesn't explode) I know that SR just runs the math and doesn't actually land your rocket anyway. @Starwaster has the right idea, it just needs to check if it can do it. If you want it to actually do a correct boostback, you can use FMRS.